select.ops.indoor

Data table merging gene(s) and operon(s) annotations. See <code>join.genes.and.operons</code>.

genes.and.operons

Transcription levels for the coding regions. See <code>comp.gene.transc.levels</code>.

transcCDSs

Transcription levels for the intergenic regions (forard strand). See <code>comp.igr.transc.levels</code>.

transcIGRs.pos

Transcription levels for the intergenic regions (reverse strand). See <code>comp.igr.transc.levels</code>.

transcIGRs.neg

wseq

verbose


Build a data table containing the transcriptomic/genomic feature values of operon pairs annotated in DOOR.
The operon classifier trained/validated on the OPs and NOPs is used to predict the operon status of these gene pairs.


internal

An implementation of the computational strategy for the
comprehensive analysis of condition-dependent operon maps in prokaryotes
proposed by Fortino et al. (2014) <DOI:10.1186/1471-2105-15-145>.
It uses RNA-seq transcriptome profiles to improve prokaryotic operon map inference.

select.ops.indoor: Define the set of OPs annotated in DOOR.

Description

Usage

Arguments